-
Notifications
You must be signed in to change notification settings - Fork 44
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Feature/morphology2 #32
base: paul_develop
Are you sure you want to change the base?
Feature/morphology2 #32
Conversation
TO DO: put in a function to catch when you use phyml "get_all_morphology_models" in phyml.py (it should return an empty list).
This update was suggested (and massively helped out) by Chris Laumer at Harvard. LG4 models are mixture models, which divide up sites based on their rates in different ways. LG4M can be combined (in RAxML) with other models in partitioned analyses, but LG4X can't. LG4M has 1 parameter (gamma rate). LG4X has six free parameters - 3 rates and 3 weights (it doesn't use a gamma rate distribution). Note that we can now fit partitioned models in partitionfinder that can't actually be used in RAxML or PhyML, because we can e.g. specify a model list that includes combinations of models that RAxML can't deal with.
this is to make sure that the default behaviour of PF is to only use lists of models that can actaully be analysed in RAxML.
This update was suggested (and massively helped out) by Chris Laumer at Harvard. LG4 models are mixture models, which divide up sites based on their rates in different ways. LG4M can be combined (in RAxML) with other models in partitioned analyses, but LG4X can't. LG4M has 1 parameter (gamma rate). LG4X has six free parameters - 3 rates and 3 weights (it doesn't use a gamma rate distribution). Note that we can now fit partitioned models in partitionfinder that can't actually be used in RAxML or PhyML, because we can e.g. specify a model list that includes combinations of models that RAxML can't deal with.
this is to make sure that the default behaviour of PF is to only use lists of models that can actaully be analysed in RAxML.
it now saves two plots as pdfs - one for downloads, one for citations
The first step to removing all of the run files.
Conflicts: partfinder/parser.py partfinder/raxml_models.py partfinder/reporter.py partfinder/subset.py
still needs more work, but this is a good start
…XML and Fast_tiger
This is a pretty big pull request, and includes ALL of Paul's stuff as well as ALL of April's stuff (right @pbfrandsen? @wrightaprilm?). I wonder if we should wait until the workshop to merge this. There are bound to be a lot of conflicts that would probably be best addressed with Paul, Brett, and myself in the room at the same time!! |
So, yes, this is all of my stuff. My code should be easily mergeable with paul_develop (it's mostly model-handling additions), but I'm not able to speak to how paul_develop relates to the rest of the code. |
OK, I'm an idiot. I thought this was the big merge into the main branch, now I see you're merging with Paul_develop. @brettc, what do you think the best way to handle this is? |
Given it is not on the main develop branch, I think this is fine as long as a) Paul is happy with it b) all tests pass. We plan to merge the morphology stuff in anyway, as well as Paul's stuff, so having it all in one place might help. It looks mostly harmless to me from a quick scan, but 2 Questions:
Brett |
|
I think this should be pretty straightforward. I will spend some time running the tests and merging the changes into the paul_develop branch early next week. Sent from my iPad
|
The threading problem sounds odd --- it shouldn't even be called when only a single thread is being used. I'll add this to our list of things to check for v2.0. |
Brett - start a new issue for the threading problem. Paul - good luck! On 1 February 2015 at 16:07, Brett Calcott notifications@github.com wrote:
Rob Lanfear phone: +61 (0)2 9850 8204 |
Just by way of an update, the paul_develop branch fails a bunch of tests by itself, so I haven't completed the merge. I'm tracking down what is going wrong in paul_develop before I merge in the morphology branch. |
Assorted features to make morphology work.